Whoever created the city, most of it apparently sank in one of the huge seismic events that this part of the Pacific Rim is famous for, Kimura said.

The world's largest recorded tsunami struck Yonaguni Jima in April 1771 with an estimated height of more than 131 feet (40 meters), he noted, so such a fate might also have befallen the ancient civilization.

Kimura said he has identified ten structures off Yonaguni and a further five related structures off the main island of Okinawa. In total the ruins cover an area spanning 984 feet by 492 feet (300 meters by 150 meters).

The structures include the ruins of a castle, a triumphal arch, five temples, and at least one large stadium, all of which are connected by roads and water channels and are partly shielded by what could be huge retaining walls.

Kimura believes the ruins date back to at least 5,000 years, based on the dates of stalactites found inside underwater caves that he says sank with the city.

And structures similar to the ruins sitting on the nearby coast have yielded charcoal dated to 1,600 years ago—a possible indication of ancient human inhabitants, Kimura added.

But more direct evidence of human involvement with the site has been harder to come by.

"Pottery and wood do not last on the bottom of the ocean, but we are interested in further research on a relief at the site that is apparently painted and resembles a cow," Kimura said.

"We want to determine the makeup of the paint. I would also like to carry out subsurface research."

Ouchi said that he has never seen tectonic activity having such an effect on a landscape either above or below the water.

"I've dived there as well and touched the pyramid," he said. "What Professor Kimura says is not exaggerated at all. It's easy to tell that those relics were not caused by earthquakes."

Boston University's Schoch, meanwhile, is just as certain that the Yonaguni formations are natural.

He suggests that holes in the rock, which Kimura believes were used to support posts, were merely created by underwater eddies scouring at depressions.

Lines of smaller holes were formed by marine creatures exploiting a seam in the rock, he said.

"The first time I dived there, I knew it was not artificial," Schoch said. "It's not as regular as many people claim, and the right angles and symmetry don't add up in many places."

He emphasizes that he is not accusing anyone of deliberately falsifying evidence.

But many of the photos tend to give a perfect view of the site, making the lines look as regular as possible, he said.

Schoch also says he has seen what Kimura believes to be renderings of animals and human faces at the site.

"Professor Kimura says he has seen some kind of writing or images, but they are just scratches on a rock that are natural," he said.

"He interprets them as being manmade, but I don't know where he's coming from."

But Kimura is undeterred by critics, adding that the new governor of Okinawa Prefecture and officials from the United Nations Educational, Scientific, and Cultural Organization have recently expressed interest in verifying the site.

"The best way to get a definitive answer about their origins is to keep going back and collecting more evidence," he continued.

"If I'd not had a chance to see these structures for myself, I might be skeptical as well."